Improving the predication efficiency of porcine production performance at early stage will contribute to reducing the breeding and production costs. The intestinal microbiota had received plenty of attention in recent years due to their influence on host health and performance. The purpose of this study was to investigate the relationship between the fecal microbiota at early growth period and porcine feed efficiency (FE) under a commercial feeding environment. Ninety-one pigs were reordered according to the residual feed intake (RFI) values between day 90 on test and day 160 off test, 9 lowest RFI pigs and 9 highest RFI pigs were selected as the LRFI group and the HRFI group, respectively. Fecal samples from pigs in the early grower phase (day 80) were performed for microbial diversity, composition, and predicted functionality by using 16S rRNA sequencing. The results showed that no significant differences in microbial alpha diversity were observed between two RFI groups, whereas, some RFI-associated compositional differences were revealed. In particular, the microbiota of the LRFI group (more feed-efficient) had significantly higher levels of some members of Clostridiales and Bacteroidales (e.g., g_1_68 and g_norank_f_p_2534_18B5), which may promoted FE through protecting gut barrier function, compared with those of the HRFI pigs. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis found that the LRFI pigs were likely have microbiota with higher levels of amino acid metabolism. Moreover, redundancy analysis (RDA) showed that litter size, parity, and date of birth had significant effects on the bacterial community structure. These results improved our knowledge of the porcine early-life fecal microbiota and its potential link underlying RFI, which would be useful for future development of microbial biomarkers for predicting and improving porcine FE as well as investigation of targets for dietary strategies.

The epigenetic regulation mechanism of porcine skeletal muscle development relies on the openness of chromatin and is also precisely regulated by transcriptional machinery. However, fewer studies have exploited the temporal changes in gene expression and the landscape of accessible chromatin to reveal the underlying molecular mechanisms controlling muscle development. To address this, skeletal muscle biopsy samples were taken from Landrace pigs at days 0 (D0), 60 (D60), 120 (D120), and 180 (D180) after birth and were then analyzed using RNA-seq and ATAC-seq. The RNA-seq analysis identified 8554 effective differential genes, among which ACBD7, TMEM220, and ATP1A2 were identified as key genes related to the development of porcine skeletal muscle. Some potential cis-regulatory elements identified by ATAC-seq analysis contain binding sites for many transcription factors, including SP1 and EGR1, which are also the predicted transcription factors regulating the expression of ACBD7 genes. Moreover, the omics analyses revealed regulatory regions that become ectopically active after birth during porcine skeletal muscle development after birth and identified 151,245, 53,435, 30,494, and 40,911 peaks. The enriched functional elements are related to the cell cycle, muscle development, and lipid metabolism. In summary, comprehensive high-resolution gene expression maps were developed for the transcriptome and accessible chromatin during postnatal skeletal muscle development in pigs.

Litter size and teat number are economically important traits in the porcine industry. However, the genetic mechanisms influencing these traits remain unknown. In this study, we analyzed the genetic basis of litter size and teat number in Bama Xiang pigs and evaluated the genomic inbreeding coefficients of this breed. We conducted a genome-wide association study to identify runs of homozygosity (ROH), and copy number variation (CNV) using the novel Illumina PorcineSNP50 BeadChip array in Bama Xiang pigs and annotated the related genes in significant single nucleotide polymorphisms and common copy number variation region (CCNVR). We calculated the ROH-based genomic inbreeding coefficients (FROH) and the Spearman coefficient between FROH and reproduction traits. We completed a mixed linear model association analysis to identify the effect of high-frequency copy number variation (HCNVR; over 5%) on Bama Xiang pig reproductive traits using TASSEL software. Across eight chromosomes, we identified 29 significant single nucleotide polymorphisms, and 12 genes were considered important candidates for litter-size traits based on their vital roles in sperm structure, spermatogenesis, sperm function, ovarian or follicular function, and male/female infertility. We identified 9,322 ROHs; the litter-size traits had a significant negative correlation to FROH. A total of 3,317 CNVs, 24 CCNVR, and 50 HCNVR were identified using cnvPartition and PennCNV. Eleven genes related to reproduction were identified in CCNVRs, including seven genes related to the testis and sperm function in CCNVR1 (chr1 from 311585283 to 315307620). Two candidate genes (NEURL1 and SH3PXD2A) related to reproduction traits were identified in HCNVR34. The result suggests that these genes may improve the litter size of Bama Xiang by marker-assisted selection. However, attention should be paid to deter inbreeding in Bama Xiang pigs to conserve their genetic diversity.

In China there are approximately 100 pig breeds, which show great diversity in their appearance. However, information on genome selection signatures, such as spine curvature, is scarce. Therefore, we used the fixation index (F ST ) and crosspopulation extended haplotype homozygosity (XPEHH) methods to explore the genome selection signatures of spine curvature in six breeds of Chinese indigenous pig. We identified 396 and 389 single nucleotide polymorphisms using the F ST and XPEHH methods, respectively. We detected 19 selection signatures and 28 genes located in the selected regions. Five candidate genes (MAP3K7, CUX1, GRIN2B, ALPL and MACF1) were identified in the selection signatures. Additionally, 719 high-frequency runs of homozygosity regions, 17 unique runs of homozygosity regions, 78 genes and 27 pathways were identified in the runs of homozygosity analysis. The TGF-beta signaling pathway and eight genes related to the spine formation, spine defects and intervertebral disk degeneration were identified, comprising ACVR1, FMOD, ITGA4, MAPK8, PDGF, RPL3, SULF1 and UBE2D1. In summary, we identified 13 candidate genes related to spine curvature in Chinese indigenous pigs.